Objective To elucidate the epidemiological characteristics of hemorrhagic fever with renal syndrome (HFRS) and associated reservoir hosts in Fujian province, China and to provide a scientific basis for the prevention and control of this disease. Methods The data on the epidemic situation of HFRS in Fujian province were subjected to statistical analysis. Rodents were captured using cages at night, and the population density and species composition of captured rodents were determined. Hantavirus antigen was detected and identified from rodent lungs by indirect immunofluorescence assay. Results A total of 373 cases of HFRS were reported in Fujian in 2012, with an incidence of 1.0027/100 000. The cases distributed in 61 counties, county?level cities, or districts, particularly in cities of Nanping, Fuzhou, Quanzhou, and Ningde. The incidence of HFRS was the highest in counties of Songxi, Zhouning, Shaowu, and Zhenghe. The surveillance of rodent populations showed that the mean trap catch rate was 5.32% indoors. The Norway rat (Rattus norvegicus), the reservoir of Soul virus, was the predominant species. In the mixed epidemic area, the mean trap catch rate of rodents was 3.62% in the field, and R. fulvescens was the predominant species. HFRS virus antigen was detected for the first time from R. norvegicus and R. tanezumi in county of Jiangle and R. norvegicus in county of Wuping. Conclusion R. norvegicus is still the main reservoir host of HFRS in Fujian. In 2012, the incidence of HFRS in Fujian increased significantly, especially in counties of Songxi county and Zhouning. Integrated rodent management should be implemented, and HFRS bivalent vaccine should be widely administered among the high risk populations, so as to reduce the incidence and prevent the outbreak of HFRS.